qunetwork {QUBIC} | R Documentation |
This function can automatically create co-expression networks along with their visualization based on identified biclusters in QUBIC. Three correlation methods, Pearson, Kendall and Spearman, are available for a user, facilitating different preferences in practical usage.
qunetwork(x, BicRes, number = 1:BicRes@Number, groups = c(number[[1]]), method = c("pearson", "kendall", "spearman"))
x |
The data matrix |
BicRes |
biclust::BiclustResult object |
number |
Which bicluster to be plotted |
groups |
An object that indicates which nodes belong together. |
method |
A character string indicating which correlation coefficient (or covariance) is to be computed. One of 'pearson' (default), 'kendall', or 'spearman', can be abbreviated. |
a list contains a weights matrix and groupinfo
# Load microarray matrix data(BicatYeast) res <- biclust::biclust(BicatYeast[1:50, ], method=BCQU(), verbose = FALSE) # Constructing the networks for the 4th and 13th identified biclusters. net <- qunetwork(BicatYeast[1:50, ], res, number = c(4, 13), group = c(4, 13), method = 'spearman') ## Not run: if (requireNamespace('qgraph')) qgraph::qgraph(net[[1]], groups = net[[2]], layout = 'spring', minimum = 0.6, color = cbind(rainbow(length(net[[2]]) - 1),'gray'), edge.label = FALSE) ## End(Not run) ## Not run: #Load microarray matrix data(BicatYeast) res <- biclust::biclust(BicatYeast[1:50, ], method=BCQU(), verbose = FALSE) # Constructing the networks for the 4th and 13th identified biclusters, # using the whole network as a background. net <- qunetwork(BicatYeast[1:50, ], res, group = c(4, 13), method = 'spearman') if (requireNamespace('qgraph')) qgraph::qgraph(net[[1]], groups = net[[2]], layout = 'spring', minimum = 0.6, color = cbind(rainbow(length(net[[2]]) - 1),'gray'), edge.label = FALSE) ## End(Not run)